The ONLY thing EU3 was better in was that the earlier start date allowed you to play over 420 years. I am sure they will add it in an expansion later though (or maybe an even earlier 1356 start date)
EU4 is superior in most aspects of the game - however the tech system is something I don't enjoy too much, since it's limiting strategies. You cannot go for an advanced army or fleet anymore while neglecting other tech trees, so you're just stuck to randomness.
Played EU3 since release pretty much non-stop. Loved the game. In my opinion EUIV is a superior game in almost every way possible. I'm up to 86 hours already, although that probably says more about the lack of my social life more than anything else.
EU3 was a very buggy product (without being game-breaking) upon release, and took many updates over many months to work that out. EU4 seems to be more a matter of tweaking. General agreement on that?
Edit: Almost forgot. THANK YOU FOR LETTING ME KNOW WHEN REBELS RANDOMLY ENTER MY LAND. Seriously, this has to be the best thing Paradox has ever done in their entire existence